The name derives from the old Jubanico family who founded the church around the year 900. It appears that fortified walls were added to the church to protect the city at the behest of Doge Tribuno in the 10th century. The fortification stretched from the outskirts of Olivolo right up to church. According to a chronicle attributed to Tiepolo, during the Chioggia-Venice war, the Venetians reintroduced the custom of throwing a chain towards the opposite bank of San Gregorio to impede the entry of enemy boats into the Canal.

From 1519, it was the custom to throw a large party on the day of Santa Maria di Zobenigo with bull and bear competitions. Ferdinand Prince of Tuscany stayed with his brother Don Carlo in the square in 1628 during one of their visits to the city. The building they stayed in stretched from Ca’ Grimani to S.M. Zobenigo.

It turns out that in the parish of S.M Zobenigo in 1379, there lived a man called Michele Steno who enters the history books for a very strange reason. At a ball held in 1355 at the house of Doge Marino Faliero, he made an indecent joke to one of the doge’s wife’s ladies-in-waiting, or, some say, to the doge’s wife herself. Once the Doge came aware of this, he had him chased from the room. Steno, intent upon revenge, carved the following on the Doge’s chair:

"Marin Falier da la bela mujer,altri la gode, e lu la mantien!"

that, from venetian language, means:

Marin Falier with the beautiful wife,others enjoy her while he maintains her"

Doge Faliero swore to avenge this insult with Steno’s blood, but was discovered and beheaded. Steno, on the other hand, on reaching old age, was in turn elected Doge in 1400.